Python Symbol Lookup Error Mkl
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Undefined Symbol: Mkl_serv_getenv
issue undefined symbol: mkl_serv_getenv in numexpr #2031 Open joshowen opened this Issue Feb mkl-rt 5, 2016 · 6 comments Projects None yet Labels None yet Milestone No milestone Assignees No libmkl_intel_thread.so: undefined symbol: omp_get_num_procs one assigned 6 participants joshowen commented Feb 5, 2016 We are not using any MKL optimized libraries, but are getting this, where we didn't previously python: symbol lookup error: /app/.heroku/miniconda/envs/heroku-env/lib/python2.7/site-packages/numexpr/../../../libmkl_vml_avx.so: undefined symbol:
Libmkl_vml_mc3.so: Undefined Symbol: Mkl_serv_getenv
mkl_serv_getenv Conda member ilanschnell commented Feb 6, 2016 This blog post: https://www.continuum.io/blog/developer-blog/anaconda-25-release-now-mkl-optimizations Describes how to not use MKL linked versions of packages (on Unix). Nevertheless, the symbol error indicates that a MKL library is missing in the linkage. We have to look into that. ozancaglayan commented Feb 9, 2016 So somehow this morning conda brought to me the mkl package and I've hit the
Python Mkl
same problem. Now I did an update --all and it downgrades some numexpr, numpy, scipy and scikit-learn and installs mkl-rt package. And it's working correctly now. 👍 1 kmdouglass commented Mar 31, 2016 I have also received this error. One of my environments needed PyTables so I performed a conda install pytables, which also upgraded a package related to MKL (I can't remember what package specifically; if you could point me towards a relevant log file I can find it.) After this, I would receive the following error message from a Jupyter Notebook session when performing matrix-heavy operations: /home/douglass/anaconda3/envs/homogenizer/bin/python: symbol lookup error: /home/douglass/anaconda3/envs/homogenizer/lib/python3.5/site-packages/numexpr/../../../libmkl_vml_mc3.so: undefined symbol: mkl_serv_getenv A conda update -all in both my root conda environment and my homogenizer environment fixed the problem like @ozancaglayan suggested above. endrebak commented May 11, 2016 The previous solution did not work for me. I had to conda install mkl-rt to avoid those errors. 👍 7 🎉 1 sharmakapil12 commented May 17, 2016 • edited Same as @endrebak for me. I had to reinstall mkl-rt. endrebak commented May 18, 2016 I got an Intel MKL FATAL ERROR: Cannot load libmkl_avx.so or libmkl_def.so someti
here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this site About Us Learn more about Stack Overflow the company Business Learn more about hiring developers or posting ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow is a community of 6.2 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign up Installing numpy-1.7.1 with MKL-10.3 https://github.com/conda/conda/issues/2031 using gcc-4.7.2 on linux up vote 2 down vote favorite I have been trying to install numpy-1.7.1 with MKL-10.3 on python-2.7.5 using gcc-4.7.2 on a linux-2.6.18-308.24.1.el5 system for a few days now. I have not long ago successfully compiled R-3.0.1 with MKL using the same compiler. I modified the site.cfg file in numpy-1.7.1 as follows: [mkl] library_dirs = /sb/software/libraries/MKL/10.3/lib/intel64 include_dirs = /sb/software/libraries/MKL/10.3/include mkl_libs = mkl_rt http://stackoverflow.com/questions/17983971/installing-numpy-1-7-1-with-mkl-10-3-using-gcc-4-7-2-on-linux lapack_libs = When I call python setup.py install, it finds the MKL libraries for BLAS and LAPACK. Up until this point, there is no complaint or warning. It breaks down once I try to do something with numpy. $ python Python 2.7.5 (default, Jul 31 2013, 16:54:43) [GCC 4.7.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import numpy >>> numpy.test('full') Running unit tests for numpy NumPy version 1.7.1 NumPy is installed in /sb/project/mjd-574/ndejay/modules/python-2.7.5/lib/python2.7/site-packages/numpy Python version 2.7.5 (default, Jul 31 2013, 16:54:43) [GCC 4.7.2] nose version 1.3.0 .................python: symbol lookup error: /sb/software/libraries/MKL/10.3/lib/intel64/libmkl_intel_thread.so: undefined symbol: omp_get_num_procs This appears to be a known issue (link to source) whereby libiomp5 is not loaded by libmkl_rt. When I add the path to libiomp5 to the library_dirs variable in site.cfg, numpy fails to detect all MKL libraries. I have even tried the following to force gcc to use its own openMP libraries/headers, but to no avail. CFLAGS='-fopenmp -lgomp' python setup.py install I would be grateful for any sort of help or advice on this matter. Do not hesitate to let me know I have omitted critical information in this thread. EDIT: I am running on
here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of http://stackoverflow.com/questions/36659453/intel-mkl-fatal-error-cannot-load-libmkl-avx2-so-or-libmkl-def-so/36967410 this site About Us Learn more about Stack Overflow the company Business https://mail.scipy.org/pipermail/numpy-discussion/2012-March/061382.html Learn more about hiring developers or posting ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow is a community of 6.2 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign undefined symbol: up Intel MKL FATAL ERROR: Cannot load libmkl_avx2.so or libmkl_def.so up vote 4 down vote favorite 4 I am running a python script and I get this error: Intel MKL FATAL ERROR: Cannot load libmkl_avx2.so or libmkl_def.so. Both files are present in the anaconda2/lib directory. How can I fix this error? Thanks. python anaconda intel-mkl share|improve this question asked Apr 16 at 2:17 undefined symbol: mkl_serv_getenv Chris Parry 127220 add a comment| 2 Answers 2 active oldest votes up vote 11 down vote if you use conda , try with two commands conda install nomkl numpy scipy scikit-learn numexpr conda remove mkl mkl-service It should fix your problem share|improve this answer answered May 1 at 13:49 Zaikun Xu 11113 the nomkl versions will be slower? –Lee Jul 4 at 17:52 add a comment| up vote 2 down vote Just wanted to note that Anaconda 4.0.0, shipped with mkl enabled by default, has this issue. The problem is indeed with Anaconda, as it can be reproduced with the simple python test below. The actual issue is that Anaconda linked with mkl, but not with libmkl_core.so, thus it has a missing symbol, and can be seen by running: $ LD_DEBUG=symbols python -c 'import sklearn.linear_model.tests.test_randomized_l1' 2>&1 | grep -i error 2200: /opt/anaconda/lib/python2.7/site-packages/scipy/special/../../../../libmkl_avx.so: error: symbol lookup error: undefined symbol: mkl_dft_fft_fix_twiddle_table_32f (fatal) I didn't want to uninstall mkl, as I'd like to have the performance boost, so I found a workaround which worked for me - preload libmkl_core.so before execution. $ python -c 'import sklearn.linear_
sorted by: [ date ] [ thread ] [ subject ] [ author ] None of that-this is why it has been so frustrating! Only thing I did was remove the folders in the ./build directory in order to get a cleaner slate, and just changed a couple libraries in site.cfg, and got the error, and it persisted even when I went back to the libraries I had given it when I got it to work. So I am really confused as to what could have caused the issue to start with. Anyways, it seems okay now-I had to add mkl_lapack to the library list. Everything isn't 100% yet, but I can now work with it. On Fri, Mar 16, 2012 at 8:35 PM, Francesc Alted